geWorkbench

The geWorkbench platform employs a component repository infrastructure to manage a large collection of pluggable components that can be used to customize the application's graphical user interface. This (ever growing) list of plug-in components covers a wide range of fucntionality for a number of different genomic data modalities.

The pluggable components in the following list are:

(a) part of the latest geWorkbench version (Released)
(b) currently actively developed (Development)
(c) currently not actively developed (Suspended)
(d) not part of geWorkbench anymore (Discontinued)

Analysis

Plugin	Status	Description
ANOVA	Released	Analysis of Variance - detection of significant differences in expression between more than two groups.
Evidence Integration	Development	A sequence and structure-based approach for functional annotation and protein-protein interaction analysis.
Hierarchical Clustering	Released	Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.
KNN	Released	k-Nearest Neighbors analysis (a GenePattern component).
Mark-Us	Released	Assesses the biochemical function for a given protein structure.
MatrixReduce	Released	Transcription Factor binding motifs.
MEDUSA	Development	The Motif Element Detection Using Sequence Agglomeration is an integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data (Leslie Lab, MSKCC).
MRA	Released	The Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis.
PCA	Released	Principal Component Analysis (a GenePattern component).
Pudge	Released	Computational protein structure prediction using sequence homology. It integrates tools used at different stages of the structural prediction process.
SkyBase	Development	Database of protein structure models produced by SkyLine based on structures solved by the NESG structural genomics consortium.
SkyLine	Development	Automated high-throughput pipeline for reverse homology-based comparative protein structure modeling based on the input template structure.
SOM	Released	Clustering of markers using Self Organizing Maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin.
SVM 3.0	Released	The Support Vector Machine is a supervised classification method that computes a maximal separating hyperplane between the expression vectors of different classes or phenotypes (a GenePattern component).
T-Test	Released	Identification of markers with statistically significant differential expression between sets of microarrays. (screenshot).
Weighted Voting	Released	Weighted Voting Analysis (a GenePattern component).

Annotation

Plugin	Status	Description
Dataset Annotation	Released	Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online notebook.
Dataset History	Released	Log of data transformations induced by data-modifying operations.
Experiment Information	Released	Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed.
Gene Ontology	Released	Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations (screenshot).
Marker Annotations	Released	Retrieval of gene and pathway information for markers on a microarray (caBIO Pathways/Cancer Gene Index); it includes visualization of BioCarta pathway diagrams (screenshot).

Data Filtering

Plugin	Status	Description
Affy Detection Call	Released	Filtering of measurements based on the value of their "detection call" attribute (Affymetrix data only) .
Deviation Filter	Released	Filtering of markers with low dynamic range.
Expression Threshold	Released	Elimination of measurements that fall outside a range of explression values.
2-channel Threshold	Released	Same as "Expression Threshold" filter but different threshold ranges can be specified for each channel (Genepix data only).
Genepix Flag Filter	Released	Filtering of measurements based on the value of their "Flags" attribute (Genepix data only).
Missing Value Filter	Released	Discards all markers that have missing measurements in more than a user specified number N of microarrays.

Data Management

Plugin	Status	Description
Marker Component	Released	Definition of data views consisting of marker subgroups. The views control the amount of data displayed.
Phenotype/Array Component	Released	Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.
Project Component	Released	Manages projects and workspaces of the user.

File Import

Plugin	Status	Description
Affymetrix CEL	Released	Loads Affymetrix probe CELl intensity files ("*.cel").
Affymetrix File Matrix	Released	Loads Affymetrix EXPperiment files ("*.exp").
Affymetrix MAS5/GCOS	Released	Loads output files from the GeneChip Operating Software formerly known as MAS5 Statistical algorithm (several different file extension).
FASTA Format	Released	Loads files that are in FASTA format ("*.fasta" and "*.txt").
Genepix File Format	Released	Loads files in GenePix Result format ("*.gpr").
PDB Structure Format	Released	Loads files in the Protein Data Base format ("*.pdb")
Tab-delimited (RMA Express Format)	Released	Loads tab-delimited files from the Robust Multichip Analysis ("*.txt")

Network Generation and Networking

Plugin	Status	Description
ARACNe	Released	The Algorithm for the Reconstruction of Accurate Cellular Networks analyses large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks (screenshot).
caArray	Released	Search and download of gene expression data from instances of caArray (NCI microarray database product).
Cancer GEMS	Development	Interface to the NCI Cancer Genetic Markers of Susceptibility project.
Cellular Networks Knowledge Base	Released	Queries an in-house repository of locally generated B-cell interaction network data and information from external databases in order to build a network of interactions for selected genes.
Cytoscape	Released	Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 1.0(screenshot).
genSpace	Released	It logs information about the analysis tools used in geWorkbench in order to enable collaboration support for the geWorkbench users.
MINDy	Released	The Modulator Inference by Network Dynamics algorithm extends ARACNe to include detecting the influence of modulators of transcription factor activity.
NetBoost	Development	NetBoost is a network characterization algorithm.

Normalization

Plugin	Status	Description
Array-Based Centering	Released	Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.
Housekeeping Normalizer	Released	Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.
Log2 Normalizer	Released	Applies a log2 transformation to all measurements in a microarray.
Marker-Based Centering	Released	Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.
Mean-Variance Normalizer	Released	Transformation of expression measurements to standard units: for every marker, the mean measurement of the marker profile (across all microarrays in an experiment) is subtracted from each measurement in the profile and the resulting value is divided by the standard deviation of the profile.
Missing Value Normalizer	Released	Replacement of missing values with consensus values.
Quantile Normalizer	Released	Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.
Threshold Normalizer	Released	Adjustment of values that fall outside a user-specified threshold.

Sequence Analysis & Visualization

Plugin	Status	Description
Alignment Results	Released	It parses and displays the results of sequence similarity searches which were run on the NCBI BLAST service.
Pattern Discovery	Released	Discovery of sequence motifs in sets of DNA and protein sequences.
Position Histogram	Released	Visualization of results from the Pattern Discovery plugin. Motif/pattern support is plotted against relative sequence position of the motif match (screenshot).
Promoter Analysis	Released	Identification of putative transcription factor binding sites in DNA sequences (screenshot). The analysis use the profiles in the JASPAR Transcription Factor Binding Profile Database.
Sequence Alignment	Released	Run jobs on the NCBI BLAST servers directly within geWorkbench.
Sequence Panel	Released	Visualization of results from the Pattern Discovery plugin, displaying the motif match location over each sequence from the input data set.
Sequence Retriever	Released	Retrieve sequences for annotated markers from Santa Cruz (nucleotide sequences) and EBI (proteins sequences).
Synteny	Discontinued	Comparison of sequence similarity between two genomic regions. The comparison results are represented as a dot matrix augmented with detailed annotation for both regions (screenshot).

Visualization

Plugin	Status	Description
Analysis Panel	Released	Framework to support numerous, individually loadable analysis methods.
ANOVA Tabular Viewer	Released	Displays the results of ANOVA analysis of gene expression data in tabular format.
CEL Image Viewer	Released	Visualization of data in Affymetrix CEL files.
Color Mosaic	Released	Heat maps for microarray expression data, organized by phenotypic or gene groupings (screenshot).
Dendrogram	Released	Tree-structured diagrams reflecting the results of hierarchical clustering analysis (screenshot).
Evidence Integration Viewer	Development	Displays the results of the Evidence Integration analysis.
Expression Profiles	Released	Line graph of genes expression profiles across several arrays/ hybridizations (screenshot).
Expression Value Distribution	Released	Distribution plot of marker expression values across one or more microarrays.
GeneWays	Released	An essential component needed to display elements in Cytoscape and ARACNe.
GO Terms Viewer	Released	Displays the results of Gene Ontology Enrichment Analysis.
Image Viewer	Released	Visualization of screenshots saved within geWorkbench (e.g. dendrograms).
Jmol	Released	Visualization of 3D protein structures from PDB files.
Mark-Us Browser	Released	Displays the results of a Mark-Us analysis.
MatrixReduce	Released	Visualization of MatrixReduce calculations using logo, chromosomal and tabular displays.
MEDUSA Viewer	Development	Displays the results of a MEDUSA analysis.
Microarray Viewer	Released	Color-gradient representation of gene expression values (screenshot).
MINDy Viewer	Released	The results of a MINDy calculation are presented in several different tabular displays and a heat map.
MRA Viewer	Released	Displays the results of the MRA in tablular and graphical form.
NetBoost Viewer	Development	Displays a Boosting Iteration Graph, Confusion Matrix and Score Table from NetBoost Analysis.
Normalization Panel	Released	Framework to support numerous, individually loadable normalization components.
PCA Viewer	Released	Displays PCA results.
Pudge Browser	Released	Visualization of Pudge results.
Scatter Plot	Released	Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values (screenshot).
SkyBase Viewer	Development	Displays the results from the SkyBase search.
SkyLine Output All	Development	Displays all models from the Skyline modeling.
SkyLine Output Each	Development	Displays each model from the Skyline modeling.
SOM Clusters Viewer	Released	Visualization of gene clusters produced by the self-organizing maps analysis (screenshot).
SVM Viewer	Released	Visualizes results obtained from classifying samples based on SVMs generated using the Gene Pattern v3 SVM service.
Tabular Microarray Viewer	Released	Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray (screenshot).
Volcano Plot	Released	Visualize fold-change vs significance (P-value) for t-test results.
Welcome Screen	Released	Introduction to geWorkbench.